Difference between revisions of "Team:Grenoble-Alpes/Composite Part"

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        <title> Lab </title>
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                background:url('https://static.igem.org/mediawiki/2017/e/e4/Labphotoigemgrenoble.jpeg') fixed;
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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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/**************** RESULTS BANNER *****************/
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            #resultsbanner{
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        <h3>Composite Part</h3>
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<div class="popup_geoloc" onclick="Function_geo()"><img class="couvlogogeo" src="https://static.igem.org/mediawiki/2017/c/c9/LogolocalisationiGEMGrenoble.png">
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                  <span class="popuptext" id="Popup_geo"> Facing back to the Etendard glacier, in between the peaks of Maurienne and the ones of Oisan. <br> Credits: Estelle Vincent
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                  </span>
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            </div>
  
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<h2 style="padding-top:2%; padding-bottom:1%; color:#27ae60;  font-size:2vw; margin: 1.5% 0.5%;"> 1. Generalities </h2>
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<h1>Composite Parts</h1>
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<h5>BBa_K2299000 is a cholera detector part, its activation allows the detection of 39bp of CTX bacteriophage RstA gene.</h5>
  
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A composite part is a functional unit of DNA consisting of two or more basic parts assembled together. <a href="http://parts.igem.org/wiki/index.php/Part:BBa_I13507">BBa_I13507</a> is an example of a composite part, consisting of an RBS, a protein coding region for a red fluorescent protein, and a terminator.
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<tr><th colspan="2">Cholerae detector part</th></tr>
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</p>
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<tr><th>Biobrick name</th><td><a href="http://parts.igem.org/Part:BBa_K2299000" id="liens" target = "_blank">BBa_K2299000</a></td></tr>
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<tr><th>RFC Compatibility</th><td>RFC 10; RFC 12; RFC 23</td></tr>
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<tr><th>Backbones </th><td>pSB1C3</td></tr>
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<tr><th>Submitted by</th><td>iGEM Grenoble-Alpes 2017 team</td></tr>
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</table></center>
  
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<p>New composite BioBrick devices can be made by combining existing BioBrick Parts (like Inverters, Amplifiers, Smell Generators, Protein Balloon Generators, Senders, Receivers, Actuators, and so on).</p>
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<h5>We - iGEM Grenoble-Alpes 2017 team- focused on the creation of a system which would enable the detection of a short sequence present in Vibrio cholerae genome. This sequence is a fragment of bacteriophage CTX DNA, involved in Vibrio cholerae’s pathogenicity by integrating a part of its own genome which contains genes for cholera toxins production.<br>
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The target is a 39 bp sequence found in CTX RstA gene (implicated in the CTX phage DNA replication and integration), present in Vibrio cholerae O1 and O139. This chosen target is flanked with AluI restriction sites, so its digestion is necessary to free the target fragment with correct length.<br>
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The detector construction that we created - a probe that binds perfectly to the target - was inserted in psB1C3 containing BBa_J04450 allowing the emission of red fluorescence. <br>
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Finally, the goal is to detect fluorescence with SnapLab: it is our homemade detection kit, displaying the results of the detection by measuring the fluorescence intensity with a smartphone.
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</h5>
  
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<br>
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<h2 style="padding-top:2%; padding-bottom:1%; color:#27ae60;  font-size:2vw; margin: 1.5% 0.5%;"> 2. Design & functioning </h2>
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<h3>Best Composite Part Special Prize</h3>
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<p>New BioBrick devices can be made by combining existing BioBrick Parts. For example, Inverters, Amplifiers, Smell Generators, Protein Balloon Generators, Senders, Receivers, Actuators, and so on. To be eligible for this award, this part must adhere to <a href="http://parts.igem.org/DNA_Submission">Registry sample submission guidelines</a> and have been sent to the Registry of Standard Biological Parts. If you have a part you wish to nominate your team for this <a href="https://2017.igem.org/Judging/Awards">special prize</a>, make sure you add your part number to your <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a> and delete the box at the top of this page.
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<h5>The design of this detector has been inspired by Cork Ireland 2015 team : they created different detectors based on the perfect complementarity of the double strand DNA.  
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Thus, we decided to create a similar detector for cholera’s pathogen.  
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</h5>
  
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<br><br>
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<h5>BBa_K2299000 has been designed in two parts:
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<b>Please note:</b> Judges will only look at the first part number you list, so please only enter ONE (1) part number in the judging form for this prize. </p>
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<li>Bioinformatics work, aiming to find a target, build a probe depending on the target, and find an appropriate plasmid backbone to carry the probe.</li>
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<br>
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<li>Construction of the detector in practice, i.e. insertion of the probe inside the chosen backbone.</li>
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<div class="highlight">
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</h5>
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<h4>Note</h4>
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<p>This page should list all the composite parts your team has made during your project. You must add all characterization information for your parts on the Registry. You should not put characterization information on this page. Remember judges will only look at the first part in the list for the Best Composite Part award, so put your best part first!</p>
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</div>
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<h5>Then the probe is activated (via a quadruple digestion) allowing the opening of a  “window” in BBa_K2299000, so the target can bind to the probe by perfect complementarity. Plasmid is re-circularized and can be transformed.<br>
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Then the red fluorescence emitted by the bacteria that incorporated the plasmid with the target is detected thanks to a smartphone camera fixed on our detection kit, SnapLab, inside which activation and binding happened.
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</h5>
  
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</div>
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<center><img src="https://static.igem.org/mediawiki/2017/9/90/GrenobleAlpesoverview.png">
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<h5 class="tfg">Figure 1: Schematic overview of the construction of the DNA detector</h5>
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</center>
  
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<h5>All the protocols can be found <a href="https://2017.igem.org/Team:Grenoble-Alpes/Protocols" id="liens">here</a>, please have a look !</h5>
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        <div style="background-color:#27ae60; padding: 2% 2%; text-align:center; margin-top: 2%;">
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            <a href="https://2017.igem.org/Team:Grenoble-Alpes/Demonstrate" id="resultsbanner" style="font-family:'Poiret One', cursive;">
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            BACK TO OUR GENERAL RESULTS
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{{Grenoble-Alpes/footer}}

Latest revision as of 16:33, 30 October 2017

Lab

Composite Part

Facing back to the Etendard glacier, in between the peaks of Maurienne and the ones of Oisan.
Credits: Estelle Vincent

1. Generalities

BBa_K2299000 is a cholera detector part, its activation allows the detection of 39bp of CTX bacteriophage RstA gene.
Cholerae detector part
Biobrick nameBBa_K2299000
RFC CompatibilityRFC 10; RFC 12; RFC 23
Backbones pSB1C3
Submitted byiGEM Grenoble-Alpes 2017 team
We - iGEM Grenoble-Alpes 2017 team- focused on the creation of a system which would enable the detection of a short sequence present in Vibrio cholerae genome. This sequence is a fragment of bacteriophage CTX DNA, involved in Vibrio cholerae’s pathogenicity by integrating a part of its own genome which contains genes for cholera toxins production.
The target is a 39 bp sequence found in CTX RstA gene (implicated in the CTX phage DNA replication and integration), present in Vibrio cholerae O1 and O139. This chosen target is flanked with AluI restriction sites, so its digestion is necessary to free the target fragment with correct length.
The detector construction that we created - a probe that binds perfectly to the target - was inserted in psB1C3 containing BBa_J04450 allowing the emission of red fluorescence.
Finally, the goal is to detect fluorescence with SnapLab: it is our homemade detection kit, displaying the results of the detection by measuring the fluorescence intensity with a smartphone.

2. Design & functioning

The design of this detector has been inspired by Cork Ireland 2015 team : they created different detectors based on the perfect complementarity of the double strand DNA. Thus, we decided to create a similar detector for cholera’s pathogen.
BBa_K2299000 has been designed in two parts:
  • Bioinformatics work, aiming to find a target, build a probe depending on the target, and find an appropriate plasmid backbone to carry the probe.
  • Construction of the detector in practice, i.e. insertion of the probe inside the chosen backbone.
    • Then the probe is activated (via a quadruple digestion) allowing the opening of a “window” in BBa_K2299000, so the target can bind to the probe by perfect complementarity. Plasmid is re-circularized and can be transformed.
    Then the red fluorescence emitted by the bacteria that incorporated the plasmid with the target is detected thanks to a smartphone camera fixed on our detection kit, SnapLab, inside which activation and binding happened.
    Figure 1: Schematic overview of the construction of the DNA detector
    All the protocols can be found here, please have a look !

    Designed by iGEM Grenoble-Alpes 2017 team | Site Map